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Yorodumi- PDB-2eqi: Solution structure of the SH3 domain from Phospholipase C, gamma 2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2eqi | ||||||
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Title | Solution structure of the SH3 domain from Phospholipase C, gamma 2 | ||||||
Components | Phospholipase C, gamma 2 | ||||||
Keywords | IMMUNE SYSTEM / HYDROLASE / SH3 domain / Phospholipase C / gamma 2 / PLCg2 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information Dectin-2 family / Toll Like Receptor 4 (TLR4) Cascade / follicular B cell differentiation / inositol trisphosphate biosynthetic process / Synthesis of IP3 and IP4 in the cytosol / regulation of calcineurin-NFAT signaling cascade / phosphatidylcholine phospholipase C activity / GPVI-mediated activation cascade / FCERI mediated MAPK activation / positive regulation of dendritic cell cytokine production ...Dectin-2 family / Toll Like Receptor 4 (TLR4) Cascade / follicular B cell differentiation / inositol trisphosphate biosynthetic process / Synthesis of IP3 and IP4 in the cytosol / regulation of calcineurin-NFAT signaling cascade / phosphatidylcholine phospholipase C activity / GPVI-mediated activation cascade / FCERI mediated MAPK activation / positive regulation of dendritic cell cytokine production / Generation of second messenger molecules / Role of phospholipids in phagocytosis / antifungal innate immune response / phosphoinositide phospholipase C / FCERI mediated Ca+2 mobilization / positive regulation of interleukin-23 production / phosphorylation-dependent protein binding / phospholipid catabolic process / cellular response to lectin / CLEC7A (Dectin-1) signaling / positive regulation of I-kappaB phosphorylation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / response to yeast / positive regulation of cell cycle G1/S phase transition / phosphatidylinositol metabolic process / cell activation / positive regulation of phagocytosis, engulfment / positive regulation of neuroinflammatory response / phosphatidylinositol phospholipase C activity / phospholipase C activity / programmed cell death / phosphatidylinositol biosynthetic process / macrophage activation involved in immune response / negative regulation of programmed cell death / regulation of canonical NF-kappaB signal transduction / positive regulation of macrophage cytokine production / DAP12 signaling / positive regulation of reactive oxygen species biosynthetic process / toll-like receptor signaling pathway / positive regulation of NLRP3 inflammasome complex assembly / response to ATP / intracellular vesicle / positive regulation of epithelial cell migration / stimulatory C-type lectin receptor signaling pathway / phosphatidylinositol-mediated signaling / response to magnesium ion / positive regulation of interleukin-10 production / positive regulation of receptor internalization / regulation of lipid metabolic process / response to axon injury / positive regulation of type I interferon production / positive regulation of calcium-mediated signaling / release of sequestered calcium ion into cytosol / lipopolysaccharide-mediated signaling pathway / cellular response to calcium ion / positive regulation of interleukin-2 production / positive regulation of interleukin-12 production / phosphotyrosine residue binding / B cell differentiation / protein tyrosine kinase binding / calcium-mediated signaling / B cell receptor signaling pathway / ruffle membrane / positive regulation of DNA-binding transcription factor activity / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / scaffold protein binding / regulation of gene expression / response to lipopolysaccharide / positive regulation of MAPK cascade / intracellular signal transduction / membrane raft / positive regulation of gene expression / perinuclear region of cytoplasm / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Qin, X.R. / Nagashima, T. / Hayahsi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the SH3 domain from Phospholipase C, gamma 2 Authors: Qin, X.R. / Nagashima, T. / Hayashi, F. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2eqi.cif.gz | 405.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2eqi.ent.gz | 338.1 KB | Display | PDB format |
PDBx/mmJSON format | 2eqi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/2eqi ftp://data.pdbj.org/pub/pdb/validation_reports/eq/2eqi | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 7574.294 Da / Num. of mol.: 1 / Fragment: SH3 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: cell-free protein synthesis / Gene: Plcg2 / Plasmid: P050815-04 / References: UniProt: Q8CIH5 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.06mM 13C, 15N-labeled protein; 20mM d-Tris-HCl (pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 293 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |